FindProblemIons: This function scans over a range of potential ions and looks...

In rramaker/CooperR2DGC: Multiple peak alignment for untargeted 2D-GCMS metabolomics analysis (Cooper Lab specific)

Description

This function scans over a range of potential ions and looks for ions that are not present in any peak or are common enough to decrease alignment quality. Can use as input to the consensus align function to avoid including these ions during alignment to speed up processing time and improve alignments

Usage

FindProblemIons(inputFile, possibleIons = c(70:600), numCores = 1,
  absentIonThreshold = 0.01, commonIonThreshold = 2, plotData = T)

Arguments

inputFile	The file path of a representative chromatof file to use in searching for ions to filter
possibleIons	A numeric vector of possible ions to search. Make sure each ion listed is present in the input file. Defaults to 70 through 600.
numCores	The number of cores to use for parallel processing. Defaults to 1
absentIonThreshold	Numeric indicating the fraction of total ion intensity an ion has to greater than in at least one peak to not be filtered as an absent ion. Defaults to 0.01.
commonIonThreshold	Numeric indicating the number of standard deviations below the mean an ion has to decrease the global metabolite similarity score to be filtered as a common ion. Defaults to 2.
plotData	Boolean. If true, relative ion impact scores will be plotted.

Value

Two column data frame identifying filtered ions and the reason they were filtered (absent or common). If plotData is TRUE, plots common ion scores. Y-axis is the z-scored number of pairwise metabolite comparisons with a similarity score greater than 50. X-axis is the ion with the filtered ions labeled in red.

Examples

FindProblemIons(inputFile=system.file("extdata", "SampleA.txt", package="CooperR2DGC"),
    possibleIons = 70:78)

rramaker/CooperR2DGC documentation built on May 28, 2019, 3:30 a.m.